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Sample GSM1752998 Query DataSets for GSM1752998
Status Public on Aug 01, 2017
Title Alzheimer's Brain Sample44
Sample type SRA
 
Source name NCI - LOW
Organism Homo sapiens
Characteristics diagnosis: Alzheimer's disease
tissue: brain
Extracted molecule total RNA
Extraction protocol RNA was extracted with the SPLIT RNA extraction kit (Lexogen GmbH, Vienna, Austria) yielding the large RNA fraction with a lower cut-off size of 150 nt. Evaluation on a Bioanalyzer RNA Nano chip (Agilent Technologies) showed medium to high RNA quality (RIN of 6.2 – 8.3). 4 µg RNA was incubated with Terminator 5´-phosphate-dependent exonuclease (Epicentre, Madison, WI, USA) to remove degraded RNA while leaving the capped, full-length mRNA intact
Per sample, 20 ng of the purified full-length total RNA were used for performing the 3’ QuantSeq Reverse protocol (Lexogen GmbH, Vienna, Austria) resulting in NGS libraries which originate from the 3’ end of polyadenylated RNA. Library generation was started by oligo(dT) priming with primers already containing the Illumina-compatible linker sequence for Read 1. After first strand synthesis the RNA was removed before the second strand synthesis was initiated by random primers which contained the corresponding Illumina-compatible linker sequence. 3’ QuantSeq generated just one fragment per transcript at the very 3’ end. The libraries were PCR amplified and barcoded in 18 cycles. Equal amounts of the 72 libraries were combined to one lane mixture.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Reference genome alignment: sequence reads in fastq format were aligned to the reference genome GRCh38 from Ensembl, repeat-masked version, complete genome, using the bowtie2 aligner version 2.2.3 and the –end-to-end and –sensitive options, to insure global alignments of the query sequences.
Alignment conversion: sequence alignment conversion from textual .sam to binary .bam files was performed with samtools version 0.1.19
Sequence trimming and primer removal was performed with the bbduk.sh utility from the BBMap project (http://sourceforge.net/projects/bbmap/). Reference file were a long polyA tail and the sequences of the Illumina truseq primer. Options: ktrim=r (trim right end), useshortkmers=t (look for shorter kmers at read tips), mink=5 (minimum length of short kmers), trimq = 10 (regions with average quality below this value will be trimmed), qtrim=t (trim reads to remove bases below both ends).
Genome_build: GRCh38
 
Submission date Jul 01, 2015
Last update date May 15, 2019
Contact name Shahar Barbash
E-mail(s) barbashshahar@gmail.com
Organization name The Rockefeller University
Lab Tom Sakmar
Street address 1230 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL16791
Series (1)
GSE70424 UTRseq_human_brain
Relations
BioSample SAMN03835357
SRA SRX1078676

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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